‘DockingProtocol’ object has no attribute ‘setup_foldtree’

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    • May 4, 2011 at 1:24 pm #898
      Anonymous

        Hi around, sorry for disturbing with my problem that I haven’t found posted or solved and if it has been solved I didn’t find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta – docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn’t work by writing:
        =========
        docking.py in ()
        15 print “setting up docking fold tree”
        16 dock_prot = DockingProtocol() #DockingProtocol object contains many useful docking functions
        —> 17 dock_prot.setup_foldtree(p)
        18 # DockingProtocol().setup_foldtree(p, “E_I”)

        19 dock_jump = 1

        AttributeError: ‘DockingProtocol’ object has no attribute ‘setup_foldtree’
        WARNING: Failure executing file:
        Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)
        =========
        I tired to execute the script by typing the commands line by line but it doesn’t work either. I also tried Linux and MacOs X versions of PyRosetta to assure that the problem is not caused by something that is not installed or distribution related. I’m sure there is some small stupid error that I do but not able at the state of being to find it out:-(.

        Thanks for helping in advance!

        Karel K

      • May 4, 2011 at 6:04 pm #5540
        Anonymous

          Sorry, the setup_foldtree method was moved. The default method (DockingProtocol().setup_foldtree(pose)) will no longer work although you can use set_autofold_tree to let the protocol take care of it. The method can now be accessed in PyRosetta from rosetta.protocols.docking.setup_foldtree and requires a Vector1 argument containing the movable jumps. For example, using test_dock.pdb:

          rosetta.protocols.docking.setup_foldtree( pose , “E_I” , Vector1(1) )

          I haven’t checked set_autofoldtee but you can try:

          DockingProtocol().set_autofold_tree = True

          We’ll fix the script soon, thanks for finding the bug. You weren’t doing anything wrong, its one of the many things that needs to be updated soon.

          Thanks,
          Evan

        • May 5, 2011 at 10:10 am #5541
          Anonymous

            Thanks, I’ve used the
            “dock_prot.set_autofold_tree=True”
            and the script goes further, then it complains about
            “recover_sidechains = ReturnSidechainMover(starting_p)”
            since it is not defined, I made it to
            “recover_sidechains = ReturnSidechainMover(p)”
            and again the script goes further but as soon as it reaches
            “docking_highres = DockingHighRes( scorefxn_high_min, dock_jump )”
            it complains again and I was not able to find out what is the option to be set, I understood that he misses one option which I could figure out, so I commented that line and the script continues. Then it reaches
            “jd.native_pose = starting_p”
            and complains, with changing it to again to
            “jd.native_pose = p”
            it proceeds and needs ‘just’ to comment out “print
            “high resolution stage docking””
            and
            “docking_highres.apply(p)”
            and finally it writes
            “docking complete!”.
            So if you could help me to resolve the highres docking stuff, I’ll be happy user:-)

            Thanks in advance!

            KK

          • May 25, 2011 at 8:25 pm #5647
            Anonymous

              If you are using the newest version of PyRosetta, try this:


              docking_highres = DockingHighResLegacy( dock_jump, scorefxn_high_min )

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